jp7b02320_si_001.pdf (1.21 MB)
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
journal contribution
posted on 2017-03-17, 00:00 authored by Lee-Ping Wang, Keri A. McKiernan, Joseph Gomes, Kyle A. Beauchamp, Teresa Head-Gordon, Julia E. Rice, William C. Swope, Todd J. Martínez, Vijay S. PandeThe
increasing availability of high-quality experimental data and
first-principles calculations creates opportunities for developing
more accurate empirical force fields for simulation of proteins. We
developed the AMBER-FB15 protein force field by building a high-quality
quantum chemical data set consisting of comprehensive potential energy
scans and employing the ForceBalance software package for parameter
optimization. The optimized potential surface allows for more significant
thermodynamic fluctuations away from local minima. In validation studies
where simulation results are compared to experimental measurements,
AMBER-FB15 in combination with the updated TIP3P-FB water model predicts
equilibrium properties with equivalent accuracy, and temperature dependent
properties with significantly improved accuracy, in comparison with
published models. We also discuss the effect of changing the protein
force field and water model on the simulation results.